Can anybody recommend solutions for preprocessing/optimizing videos for animal tracking?
I want to crop, overlay with a mask and change contrast/brightness to make the animal tracking more robust.
There are many possible solutions for this but I wonder if anybody has developed a workflow for video preprocessing that they would recommend - free/open software preferred (i.e. imageJ or ffmpeg).
Can you provide a link to an example video? There are lots of animals.
For me, I would use high contrast background, e.g. white background for black mice. Then I would use Gaussian filter and then thresholding the video to a binary image. Then the tracking would be incredibly stable.
You don't need high contrast when using BehaviorCloud. Maybe you could try that? Or you can use iMovie (if on mac).
Thank you for your answers!
I work with fish in a backlit setup with an hourglass-like shape (see attached screenshot). As I have large datasets (over 24h of video per animal), I can't personally survey every second of the tracking process. Thus, I'd like to make the tracking most reliable by pre-processing the videos in a standardized way. I found that various tracking software - as awesome as the fact is that there's free and open tracking software - is often slow and prone to crashes if the video files are large. So I wondered if it makes sense to first optimize all my videos and then feed them to the tracking software without many adjustments.
Robert Mahar - I'm currently in the field but I'll see if I can supply a short snippet from a video
Guangwei Zhang - Do you use a commercial software or custom written scripts (python etc)?
Chloe Powell - As the amount of data is massive, I'm not sure whether a cloud-based application would be right for me.
My favorite tracker so far is the Biotracker from the IGB which seems most reliable and user-friendly (so that e.g. an undergrad can do a project with videotracking, too):
https://www.igb-berlin.de/en/biotracker
Stefan Mucha I used customized software written in python 3.4. You may check the method and supplementary Fig. S1 in:
Article Transforming Sensory Cues into Aversive Emotion via Septal-H...
For long term behavior monitoring (days and weeks), the software would record videos in 20min short clips, then a batch processing can be applied to the folder that would not kill the computer RAM.
Now, the tracking software is a command line tool, I am working on generating a GUI for it and plan to release it (freely) by the end of the year.
Hi, you can check the link below regarding the source code for the animal tracking.
https://github.com/GuangWei-Zhang/TraCon-Toolbox
Hi Stefan Mucha , pre-print is now available in Biorxiv: Preprint Track-Control, an automatic video-based real-time closed-loo...
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